Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years


Posted by Web Master (April 26, 2023)

New Mascot Server release history page

We’ve added a summary of the Mascot Server release history to the technical support page. The list includes the release date as well as links to the release announcement, overview of new features, any blog or ASMS user meeting content describing the new version and the latest available patch. All the information has always been available in the news, blog and technical support section of this website, but having everything in one place makes it much easier to find.

Posted by Web Master (April 20, 2023)

25th anniversary of Matrix Science

Matrix Science was founded in 1998, which makes this year our 25th anniversary! We have added a brand new About page, which details the company timeline, and there is a bit more history in the blog article 25 years of Matrix Science.

Thank you for your trust, custom, bug reports, ideas and feedback over the past quarter century.

Posted by Web Master (November 22, 2022)

Moving old searches to cold storage

When you submit a free search on the public Mascot server, the search results are stored on the server for a certain time, but we don’t guarantee they will be kept indefinitely. The size of the search archive has increased substantially since the limits were increased in March 2020. In order to avoid running out of storage space, we are implementing a new archival policy.

In upcoming months, we will gradually move some of the historic archive into cold storage. There will be a news announcement for each archival event. The search results will not be deleted permanently, but they will no longer be available online at

The archival policy only affects Mascot running on our public website. If you have an in-house licence, the above policy does not apply.

On 1 December 2022, we will start by moving all public Mascot searches up to 1 Jan 2010 to cold storage. If you submitted a search before 1 Jan 2010 and would like to download a copy after the archival, please send us an e-mail and we can send you the results file.

Posted by Web Master (October 12, 2022)

Mascot Distiller 2.8.3 patch release

Mascot Distiller 2.8.3 is a new patch release.

This release includes a number of important bug fixes, and we advise all users to install it.

  • 14151: Check to see if display changes require requantitation is over-sensitive
  • 14200: Protein descriptions in ANOVA plus Clustering report table are wrong
  • 14202: Unclustered Table Headers in Hierarchical Clustering Report
  • 14205: Table Peptides Report has incorrect protein ratios
  • 14220: Time alignment offset calculation incorrect in some cases
  • 14228: Creating a new project when connected to Mascot 2.6 or earlier fails
  • 14232: Crash if using normalisation to specified proteins

Please do not hesitate to contact us with any questions.

Posted by Web Master (August 31, 2022)

Mascot Server 2.8.2 patch release

Mascot Server 2.8.2 has been released. Updates from 2.8.0 and 2.8.1 for both Windows and Linux can be downloaded from the support page.

This patch release fixes two bugs related to setting up UniProt proteomes in Database Manager, three regressions introduced in version 2.8.1 and one bug with error tolerant top-down searches in cluster mode.

  • 13883: Error tolerant top-down search with >1000 queries fails in cluster mode
  • 14085: Exporting results when preferred taxonomy is selected fails with: Can’t use an undefined value as a HASH reference at ExportDat/ line 746.
  • 14086: Use of uninitialized value in subroutine entry at cgi/ line 469.
  • 14107: Error when opening results with Reporter or Multiplex quantitation in
  • 14174: Warning “Remote source does not exist” after creating database using a template, preventing scheduled database updates
  • 14184: If remote source returns neither Last-Modified nor ETag HTTP header, Database Manager fails to download updated data

More detail on the UniProt proteomes change can be found in Downloading UniProt proteomes via new API.

Please do not hesitate to contact us with any questions.

Posted by Web Master (July 11, 2022)

New pricing for updating older Mascot Server licences

We are reducing the price for updating Mascot Server 2.4 and earlier licences. The cost to update Mascot to the latest version is determined by how many versions behind your licence is. One-version update is 25%, 2-version 50% and 3-version update 75% of the cost of a new licence. For example, updating from Mascot 2.7 to 2.8 is a 1-version update, so you are paying 75% less than buying a new licence.

From 11 July 2022, the cost for 4-version update is now fixed at 90% of the cost of a new licence. Updating from version 2.3, 2.2 and earlier is treated as a 4-version update, no matter how old the licence. In other words, you now get a 10% price reduction by trading in Mascot 2.4 or older for 2.8.

This is an excellent time to update. Mascot 2.8 not only supports the latest versions of Windows and Linux, but all updates come with one year of Premium Support. If you have any trouble updating Mascot or migrating to new hardware, we are here to help you. Full benefits are:

  • Priority technical support by email (preferred) or phone
  • One free platform swap between Linux and Windows (if desired)
  • Remote problem diagnosis if deemed necessary
  • Run a 1 cpu ‘test server’ in addition to a ‘production server’, provided the licence is for 8 cpu or more
  • Automatically receive any new Mascot release

And updating grants access to a number of features and improvements:

Please contact us to request a quote or if you have any questions.

Posted by Web Master (June 10, 2022)

Mascot Distiller 2.8.2 patch release

Mascot Distiller 2.8.2 is a new patch release.

This release includes a number of important bug fixes, and we advise all users to install it. In addition, it adds support for fractionated label-free quantitation datasets.

Please do not hesitate to contact us with any questions.